Germination and Polishing Reshape Microbial Communities in Japonica and Indica Rice

Germination is a process used to improve the nutritional quality of rice. However, its impact on rice microbiomes remains poorly understood. This study evaluated the microbiota of two rice ecotypes, low-amylose (Mochi) and high-amylose (BRS Formoso), after germination and polishing using 16S rRNA and ITS amplicon sequencing. Bacterial alpha diversity was highest in commercial brown rice (Shannon index 3.21) and lowest in commercial polished rice (1.50). Beta diversity indicated that germination exerted a similar effect on bacterial community composition in both ecotypes. Principal Coordinate Analysis suggested that polishing did not markedly influence microbiome composition relative to germination. The microbial profiles of Mochi and BRS Formoso were dominated by Pantoea, Pseudomonas, Rhizopus, and Moesziomyces. Overall, germination strongly influenced bacterial and fungal communities, emerging as the main factor shaping microbial structure and dynamics. These findings provide new insights into how processing affects the rice microbiome, with implications for food quality and safety.